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DiverseSelector/methods/base.py

@@ -27,6 +27,10 @@
 
 import numpy as np
 
+__all__ = [
+    "SelectionBase"
+]
+
 
 class SelectionBase(ABC):
     """Base class for selecting subset of sample points."""

book/content/_build/.doctrees/glue_cache.json

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+{}

book/content/_build/html/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 4d0fd851dc687574c8ed135c99921c4a
+tags: 645f666f9bcd5a90fca523b33c5a78b7

book/content/_build/html/_panels_static/panels-variables.06eb56fa6e07937060861dad626602ad.css

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+:root {
+--tabs-color-label-active: hsla(231, 99%, 66%, 1);
+--tabs-color-label-inactive: rgba(178, 206, 245, 0.62);
+--tabs-color-overline: rgb(207, 236, 238);
+--tabs-color-underline: rgb(207, 236, 238);
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book/content/_build/html/_sources/base.rst

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+Base class
+=============
+.. automodule:: DiverseSelector.base
+    :members:

book/content/_build/html/_sources/dissimilarity.rst

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+Dissimilarity based methods
+=============
+.. automodule:: DiverseSelector.dissimilarity
+    :members:

book/content/_build/html/_sources/installation.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "f1be9e2f",
+   "metadata": {},
+   "source": [
+    "# Installation & Testing\n",
+    "\n",
+    "1. To install DiverseSelector using the conda package management system, install [miniconda](https://conda.io/miniconda.html) or [anaconda](https://www.anaconda.com/download) first, and then:\n",
+    "\n",
+    "```\n",
+    "    # Create and activate myenv conda environment (optional, but recommended)\n",
+    "    conda create -n myenv python=3.6\n",
+    "    conda activate myenv\n",
+    "\n",
+    "    # Install the stable release.\n",
+    "    conda install -c theochem qc-\n",
+    "```\n",
+    "2. To install DiverseSelector with pip, you may want to create a [virtual environment](https://docs.python.org/3/tutorial/venv.html), and then:\n",
+    "\n",
+    "```\n",
+    "    # Install the stable release.\n",
+    "    pip install qc-\n",
+    "```\n",
+    "\n",
+    "# Dependencies\n",
+    "\n",
+    "The following dependencies are required to run DiverseSelector properly,\n",
+    "\n",
+    "* Python >= 3.6: http://www.python.org/ \n",
+    "* NumPy >= 1.21.5: http://www.numpy.org/\n",
+    "* SciPy >= 1.5.0: http://www.scipy.org/\n",
+    "* PyTest >= 5.3.4: https://docs.pytest.org/\n",
+    "* PyTest-Cov >= 2.8.0: https://pypi.org/project/pytest-cov/\n",
+    "\n",
+    "# Testing\n",
+    "\n",
+    "The tests are automatically run when we build packages with conda, but you may try them again on your own machine after installation.\n",
+    "\n",
+    "With Ana- or Miniconda:\n",
+    "```\n",
+    "# Install pytest in your conda env.\n",
+    "conda install pytest pytest-xdist\n",
+    "# Then run the tests.\n",
+    "pytest --pyargs diverseselector -n auto\n",
+    "```\n",
+    "\n",
+    "With Pip:\n",
+    "```\n",
+    "# Install pytest in your conda env ...\n",
+    "pip install pytest pytest-xdist\n",
+    "# .. and refresh the virtual environment.\n",
+    "# This is a venv quirk. Without it, pytest may not find IOData.\n",
+    "deactivate && source ~/diverseselector/activate\n",
+    "\n",
+    "# Alternatively, install pytest in your home directory.\n",
+    "pip install pytest pytest-xdist --user\n",
+    "\n",
+    "# Finally, run the tests.\n",
+    "pytest --pyargs diverseselector -n auto\n",
+    "```"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

book/content/_build/html/_sources/intro.md

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+<!-- #region -->
+# Welcome to QC-Selector
+
+
+## Discover the Power of Diversity in Molecule Selection
+
+Are you struggling to find the optimal subset of molecules for your research or development projects? Look no further! Diverse Selector is the ultimate software package designed to help you effortlessly identify the most diverse subset of molecules from your dataset.
+
+## Why QC-Selector?
+
+In the world of chemistry, selecting the right subset of molecules is critical for a wide range of applications, including drug discovery, materials science, and molecular optimization. QC-Selector offers a cutting-edge solution to streamline this process, empowering researchers, scientists, and developers to make smarter decisions faster.
+
+## Key Features
+1. Import Your Dataset: Simply import your molecule dataset in various file formats, including SDF, SMILES, and InChi, to get started.
+2. Define Selection Criteria: Specify the desired level of diversity and other relevant parameters to tailor the subset selection to your unique requirements.
+3. Run the Analysis: Let QC-Selector's powerful algorithms process your dataset and efficiently select the most diverse molecules.
+4. Export: Explore the diverse subset and export the results for further analysis and integration into your projects.
+<!-- #endregion -->

book/content/_build/html/_sources/partition.rst

@@ -0,0 +1,5 @@
+Partition based methods
+=============
+
+.. automodule:: DiverseSelector.partition
+    :members:

book/content/_build/html/_sources/utils.rst

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+Utilities
+=============
+.. automodule:: DiverseSelector.utils
+    :members: